The bad weather -- which is expected to last for the rest of the week -- struck the east, north and south, claiming lives in four of South Africa's nine provinces, said the department in charge of disaster management, COGTA.
The famed Kruger National Park, a tourist magnet bordering Mozambique and the largest reserve in South Africa, was badly affected, COGTA spokesman Lungi Mtshali told AFP.
Mpumalanga province, in northeast South Africa, "seems to be hardest hit so far. Kruger is really bad," said Mtshali.
He said the death toll had risen to 12, up from seven on Monday.
Kruger is crossed by several rivers, which have been swollen by torrential rains since last weekend, according to the South African Weather Service (SAWS).
"Movement inside the park is restricted as some roads are damaged," said Isaac Phaahla, a spokesman for the national parks' authority, SANParks.
Several camps inside the reserve have been evacuated as a precaution.
Heavy rains started to fall last week after a cold snap in the middle of the austral summer, according to the weather service.
Some areas saw more than 20 centimetres (nearly eight inches) of rain in one day, SAWS forecaster Puseletso Mofokeng told AFP.
The deluge is expected to last for the rest of the week, Mofokeng said, warning more flooding was likely.
On Monday, the presidency declared a state of national disaster to coordinate the response and provide "temporary shelters, food and blankets" to the homeless.
The floods have inundated homes and swept away vehicles, it said. Roads, bridges and even a hospital have been affected.
Last year, South Africa was hit by its worst floods in living memory, which left more than 400 people dead in Durban, the country's third-largest city, and its surrounding areas.
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